Difference between revisions of "Sandbox"

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* '''Description:''' DNA gyrase (subunit A) <br/><br/>
+
* '''Description:''' [[16S rRNA]]<br/><br/>
 +
 
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''gyrA''
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|''rrnO-16S''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''nalA ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || DNA gyrase (subunit A)
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|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal RNA-16S
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || DNA supercoiling, <br/>initation of replication cycle and DNA elongation
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|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00070 GyrA]
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|style="background:#ABCDEF;" align="center"| '''Gene length''' || 1553 bp
 +
|-|-
 +
 
 +
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrA]]'', ''[[trnO-Ile]]''
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=GyrA GyrA]
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rrnO-16S_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 +
|style="background:#FAF8CC;" align="center"|''' '''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 91 kDa, 5.215 
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|colspan="2" | '''Genetic context''' <br/> [[Image:rrnO-16S_context.gif]]
−
|-
 
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2463 bp, 821 aa
 
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|-
 
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gyrB]]'', ''[[rrnO-16S]]''
 
−
|-
 
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|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU00070 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU00070 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU00070 DNA_with_flanks]
 
−
|-
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:GyrA_context.png]]
 
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
−
|-
 
−
|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrA_6994_9459_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:gyrA_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU00070]]
 
 
|-
 
|-
 
|}
 
|}
  
 
__TOC__
 
__TOC__
−
<br/><br/><br/><br/>
+
 
−
<br/><br/><br/><br/>
+
<br/><br/><br/><br/><br/><br/>
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<br/><br/><br/><br/>
 
−
<br/><br/>
 
  
 
= [[Categories]] containing this gene/protein =
 
= [[Categories]] containing this gene/protein =
−
{{SubtiWiki category|[[DNA condensation/ segregation]]}},
+
{{SubtiWiki category|[[translation]]}}
−
{{SubtiWiki category|[[essential genes]]}}
 
  
 
= This gene is a member of the following [[regulons]] =
 
= This gene is a member of the following [[regulons]] =
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU00070
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
=== Database entries ===
  
−
=== Database entries ===
+
* '''DBTBS entry:''' no entry
  
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* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gyrA.html]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00005]
  
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10071]
+
* '''Structure:'''
  
 
=== Additional information===
 
=== Additional information===
  
  
−
 
−
 
−
=The protein=
 
−
 
−
=== Basic information/ Evolution ===
 
−
 
−
* '''Catalyzed reaction/ biological activity:''' ATP-dependent breakage, passage and rejoining of double-stranded DNA (according to Swiss-Prot)
 
−
 
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* '''Protein family:''' topoisomerase gyrA/parC subunit family (according to Swiss-Prot)
 
−
 
−
* '''Paralogous protein(s):''' [[ParC]]
 
−
 
−
=== Extended information on the protein ===
 
−
 
−
* '''Kinetic information:'''
 
−
 
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* '''Domains:'''
 
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* '''Modification:'''
 
−
 
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* '''Cofactor(s):'''
 
−
 
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* '''Effectors of protein activity:'''
 
−
 
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* '''[[SubtInteract|Interactions]]:'''
 
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** [[GyrA]]-[[GyrB]]
 
−
 
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* '''[[Localization]]:'''
 
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** Nucleoid (Homogeneous) [http://www.ncbi.nlm.nih.gov/sites/entrez/16479537 PubMed]
 
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** nucleoid-associated in actively growing cells [http://www.ncbi.nlm.nih.gov/sites/entrez/9539793 PubMed]
 
−
 
−
=== Database entries ===
 
−
 
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* '''Structure:'''
 
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** [http://www.rcsb.org/pdb/explore/explore.do?structureId=4DDQ 4DDQ] (DNA gyrase A-subunit lacking the C-terminal DNA-wrapping domains) {{PubMed|23602808}}
 
−
 
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* '''UniProt:''' [http://www.uniprot.org/uniprot/P05653 P05653]
 
−
 
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* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU00070]
 
−
 
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* '''E.C. number:'''
 
−
 
−
=== Additional information===
 
−
 
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:* subject to Clp-dependent proteolysis upon glucose starvation {{PubMed|17981983}}
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:''' ''gyrA'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
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* '''Operon:''' ''rrnO'' operon (''[[rrnO-16S]] - [[trnO-Ile]] - [[trnO-Ala]] -[[rrnO-23S]] - [[rrnO-5S]]'') [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
−
 
 
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* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=gyrA_6994_9459_1 gyrA] {{PubMed|22383849}}
 
  
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* '''[[Sigma factor]]:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2987848 PubMed]
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
 +
** passive transcriptional regulation by cellular GTP concentration
 +
** downregulated by stringent response upon amino acid starvation {{PubMed|21097612}}
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed],  GyrA is subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
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=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Dagmar Klostermeier]], Biozentrum Basel, Switzerland [http://www.biozentrum.unibas.ch/klostermeier/index.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
  
 
=References=
 
=References=
−
<pubmed>16479537,17981983 ,9539793 , 2987848  19666507 17320901 23475963 23602808 20870749</pubmed>
+
'''Additional publications:''' {{PubMed|21097612,21303765}}
−
 
+
<pubmed> 6312418, 19447912 15496987 20634236 </pubmed>  
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[[Category:Protein-coding genes]]
+
[[Category:Ribosomal RNA]]

Revision as of 14:40, 11 November 2013

Gene name rrnO-16S
Synonyms
Essential no
Product ribosomal RNA-16S
Function translation
Gene length 1553 bp
Immediate neighbours gyrA, trnO-Ile
Gene sequence (+200bp)
Genetic context
RrnO-16S context.gif
This image was kindly provided by SubtiList







Categories containing this gene/protein

translation

This gene is a member of the following regulons

The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]
  • Structure:

Additional information

Expression and regulation

  • Regulation:
    • passive transcriptional regulation by cellular GTP concentration
    • downregulated by stringent response upon amino acid starvation PubMed
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

Additional publications: PubMed

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